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Michelle Surma

on 18 December 2012

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Transcript of AP BIOLOGY

BIG IDEAS BIG IDEA 2 SUCCESS IN AP BIOLOGY Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. BIG IDEA 1 Living systems store, retrieve, transmit, and respond to information essential to life processes. BIG IDEA 4 Biological systems interact, and these systems and their interactions possess complex properties. BIG IDEA 3 The process of evolution drives the diversity and unity of life. There is both negative and positive feedback present in mechanisms. Positive feedback mechanisms maintain dynamic homeostasis for a particular condition by regulating physiological processes, returning the changing condition back to its target set point. Negative feedback mechanisms amplify responses and processes in biological organisms. The variable initiating the response is moved farther away from the initial set- point. Amplification occurs when the stimulus is further activated, which , in turn, initiates an additional response that produces a system change. Continuity of homeostatic mechanisms reflects common ancestry, while changes may occur in response to different environmental conditions. Immune systems of animals, both vertebrate and invertebrate are complex. Vertebrate immune systems
have nonspecific and
nonheritable defense
mechanisms against
pathogens. Mammals use specific immune
responses triggered by natural
or artificial agents that disrupt
dynamic homeostasis. The mammalian immune system includes two types of specific responses: Cell mediated Humoral In the cell-mediated response, cytotoxic T cells, a type of lymphocytic white blood cell, target intracellular pathogens when antigens are displayed on the outside of the cells. In the humoral response, B cells, a type of lymphocytic white blood cell, produce antibodies against specific antigens. Contain: Antigens are recognized by antibodies to the antigen. Antibodies are proteins produced by B cells, and each antibody is specific to a particular antigen. A second exposure to an antigen results in a more rapid and enhanced immune response. Genetic information is transmitted from one generation to the next through DNA or RNA. Genetic information is stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules. Noneukaryotic organisms Eukaryotic organisms There are some exceptions within biology. Contain circular chromosomes Contain multiple linear chromosomes Prokaryotes, viruses and eukaryotes can contain plasmids, which are small extra-chromosomal, double-stranded circular DNA molecules. The proof that DNA is the carrier of genetic information involved a number of important historical experiments. i. Contributions of Watson, Crick, Wilkins, and Franklin on the structure of DNA ii. Avery-MacLeod-McCarty experiments iii. Hershey-Chase experiment DNA replication ensures continuity of hereditary information. Replication is a semiconservative process; that is, one strand serves as the template for a new, complementary strand. Replication requires DNA polymerase plus many other essential cellular enzymes, occurs bidirectionally, and
differs in the production of the leading and lagging strands. Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny. DNA and RNA molecules have structural similarities and differences that define function. Both have three components — sugar, phosphate and a nitrogenous base — which form nucleotide units that are
connected by covalent bonds to form a linear molecule with 3'and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone. The basic structural differences include:
i. DNA contains deoxyribose (RNA contains ribose).
ii. RNA contains uracil in lieu of thymine in DNA.
iii. DNA is usually double stranded, RNA is usually single stranded.
iv. The two DNA strands in double-stranded DNA are antiparallel in directionality. Both DNA and RNA exhibit specific nucleotide base pairing that is conserved through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine(C-G). Purines (G and A) have a double ring structure. Pyrimidines (C, T and U) have a single ring structure. RNA The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function. mRNA tRNA rRNA carries information from the DNA to the ribosome. bind specific amino acids and allow information in the mRNA to be translated to a linear peptide sequence. functional building blocks of ribosomes. The role of RNAi includes regulation of gene expression at the level of mRNA transcription. The enzyme RNA-polymerase reads the DNA molecule in the 3' to 5' direction and synthesizes complementary mRNA molecules that determine the order of amino acids in the polypeptide. In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications. (addition of a poly-A tail, addition of a GTP cap, excision of introns) Translation of the mRNA occurs in the cytoplasm on the ribosome. In prokaryotic organisms, transcription is coupled to translation of the message. Translation involves energy and
many steps, including initiation, elongation and termination. The mRNA interacts with the rRNA of the ribosome to initiate translation at the (start) codon. The sequence of nucleotides on the mRNA is read in triplets called codons. Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids have more than one codon. tRNA brings the correct amino acid to the correct place on the mRNA. The amino acid is transferred to the growing peptide chain. Phenotypes are determined through protein activities. Genetic engineering techniques can manipulate the heritable information of DNA and, in special cases, RNA. Mitosis The cell cycle is a complex set of stages that is highly regulated with checkpoints, which determine the ultimate fate of the cell. Interphase consists of three phases: growth, synthesis of DNA, preparation for mitosis. The cell cycle is directed by internal controls or checkpoints. Internal and external signals provide stop-and-go signs at the checkpoints. Cyclins and cyclin-dependent kinases control the cell cycle. Mitosis alternates with interphase in the cell cycle. When a cell specializes, it often enters into a stage where it no longer divides, but it can reenter the cell cycle when given appropriate cues. Nondividing cells may exit the cell cycle; or hold at a particular stage in the cell cycle. Mitosis passes a complete genome from the parent cell to daughter cells. Mitosis occurs after DNA replication. Mitosis followed by cytokinesis produces two genetically identical daughter cells. Mitosis plays a role in growth, repair, and asexual reproduction. Mitosis is a continuous process with observable structural features along the mitotic process. Meiosis Meiosis, a reduction division, followed by fertilization ensures genetic diversity in sexually reproducing organisms. Meiosis ensures that each gamete receives one complete haploid (1n) set of chromosomes. During meiosis, homologous chromosomes are paired, with one homologue originating from the maternal parent and the other from the paternal parent. Orientation of the chromosome pairs is random with respect to the cell poles. Separation of the homologous chromosomes ensures that each gamete receives a haploid (1n) set of chromosomes composed of both maternal and paternal chromosomes. During meiosis, homologous chromatids exchange genetic material via a process called “crossing over,” which increases genetic variation in the resultant gametes. Fertilization Fertilization involves the fusion of two gametes, increases genetic variation in populations by providing for new
combinations of genetic information in the zygote, and restores the diploid number of chromosomes. Rules of probability can be applied to analyze passage of single gene traits from parent to offspring. Segregation Segregation and independent assortment of chromosomes result in genetic variation. Segregation and independent assortment can be applied to genes that are on different chromosomes. Genes Genes that are adjacent and close to each other on the same chromosome tend to move as a unit; the probability that they will segregate as a unit is a function of the distance between them. The pattern of inheritance (monohybrid, dihybrid, sex-linked, and genes linked on the same homologous chromosome) can often be predicted from data that gives the parent genotype/phenotype and/or the offspring phenotypes/genotypes. Certain human genetic disorders can be attributed to the inheritance of single gene traits or specific chromosomal changes, such as nondisjunction. Patterns of inheritance of many traits do not follow ratios predicted by Mendel’s laws and can be identified by quantitative analysis, where observed phenotypic ratios statistically differ from the predicted ratios. Inheritance Some traits are determined by genes on sex chromosomes which reside on sex chromosomes (X in humans). In mammals and flies, the Y chromosome is very small and carries few genes. In mammals and flies, females are XX and males are XY; as such, X-linked recessive traits are always expressed in males. Some traits are sex limited, and expression depends on the sex of the individual, such as milk production in female mammals and pattern baldness in males. Signal transmission within and between cells mediates gene expression and between cells it mediates cell
function. DNA Alterations in a DNA sequence can lead to changes in the type or amount of the protein produced and the consequent phenotype. DNA mutations can be positive, negative or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein. Errors in DNA replication or DNA repair mechanisms, and external factors, including radiation and reactive chemicals, can cause random changes, e.g., mutations in the DNA. Changes in chromosome number often result in new phenotypes, including sterility caused by triploidy and
increased vigor of other polyploids. Changes in chromosome number often result in human disorders with developmental limitations, including Trisomy 21 (Down syndrome) and XO (Turner syndrome) Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected by environmental conditions. The imperfect nature of DNA replication and repair increases variation. The horizontal acquisitions of genetic information primarily in prokaryotes via transformation (uptake of naked DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer) and transposition (movement of DNA segments within and between DNA molecules) increase variation. Sexual reproduction in eukaryotes involving gamete formation, including crossing-over during meiosis and the random assortment of chromosomes during meiosis, and fertilization serve to increase variation. Reproduction processes that increase genetic variation are evolutionarily conserved and are shared by various organisms. Viruses Viral replication differs from other reproductive strategies and generates genetic variation via various mechanisms. Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes. Viruses replicate via a component assembly model allowing one virus to produce many progeny simultaneously via the lytic cycle. Virus replication allows for mutations to occur through usual host pathways. RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation. Related viruses can combine/recombine information if they infect the same host cell. HIV is a well-studied system where the rapid evolution of a virus within the host contributes to the pathogenicity of viral infection. The reproductive cycles of viruses facilitate transfer of genetic information. Viruses transmit DNA or RNA when they infect a host cell. (transduction in bacteria, transposons present in incoming DNA) Some viruses are able to integrate into the host DNA and establish a latent (lysogenic) infection. These latent viral
genomes can result in new properties for the host such as increased pathogenicity in bacteria Signal Transduction Correct and appropriate signal transduction processes are generally under strong selective pressure. In single-celled organisms, signal transduction pathways influence how the cell responds to its environment. Use of chemical messengers by microbes to communicate with other nearby cells and to regulate specific pathways in response to population density (quorum sensing) Use of pheromones to trigger reproduction and developmental pathways Response to external signals by bacteria that influences cell movement In multicellular organisms, signal transduction pathways coordinate the activities within individual cells that support the function of the organism as a whole. (e.g. epinephrine stimulation of glycogen breakdown in mammals) Immune cells interact by cell-cell contact, antigen-presenting cells (APCs), helper T-cells and killer T-cells. Cells communicate over short distances by using local regulators that target cells in the vicinity of the emitting cell. Endocrine signals are produced by endocrine cells that release signaling molecules, which are specific and can travel long distances through the blood to reach all parts of the body. Signaling begins with the recognition of a chemical messenger, a ligand, by a receptor protein. Different receptors recognize different chemical messengers, which can be peptides, small chemicals or proteins, in a specific one-to-one relationship. A receptor protein recognizes signal molecules, causing the receptor protein’s shape to change, which initiates transduction of the signal. Signal transduction is the process by which a signal is converted to a cellular response. Signaling cascades relay signals from receptors to cell targets, often amplifying the incoming signals, with the result of appropriate responses by the cell. Second messengers such as cyclic AMP, Calcium and IP3 are often essential to the function of the phosphorylation cascade. Many signal transduction pathways include protein. Phosphorylation cascades in which a series of protein kinases add a phosphate group to the next protein in the cascade sequence. Neurons The neuron is the basic structure of the nervous system that reflects function. A typical neuron has a cell body, axon and dendrites. Many axons have a myelin sheath that acts as an electrical insulator. The structure of the neuron allows for the detection, generation, transmission and integration of signal information. Schwann cells, which form the myelin sheath, are separated by gaps of unsheathed axon over which the impulse travels as the signal propagates along the neuron. Action potentials propagate impulses along neurons. Membranes of neurons are polarized by the establishment of electrical potentials across the membranes. In response to a stimulus, Na+ and K+ gated channels sequentially open and cause the membrane to become locally depolarized. Na+/K+ pumps, powered by ATP, work to maintain membrane potential. Transmission of information between neurons occurs across synapses. In most animals, transmission across synapses involves chemical messengers called neurotransmitters. Transmission of information along neurons and synapses results in a response. The response can be stimulatory or inhibitory. Homeostasis Division of cells such as muscle, skin, blood, etc. Division of sex cells (DNA replication) DNA polymerase A- Adenine
G- Guanine C- Cytosine
T- Thymine
U- Uracil Replication Lagging Strand Goes away from replication fork Okazaki Fragments Leading strand Goes toward their replication fork 5' to 3' direction Semiconservative process Nondisjunction Independent
Assortment Segregation Dominant or Recessive Nervous System Central Nervous System Brain Spine Peripheral Nervous System Extends throughout the body Sympathetic system is involved in arousal Parasympathetic system is involved in bringing the body back to homeostasis UCA!
The Universal Common
Ancestor is the genetic origin of life. Competition spawns diversity among organisms. If a phenotype proves to be more useful for the survival of a species, that phenotype will likely be passed on to future generations while less resourceful traits are lost. The science word for successfully produces offspring is evolutionary fitness. Genetic variations are often results of mutations that prove useful for evolutionary fitness. Natural selection is the main driving force in evolution, but often in smaller populations random happenstances are also factors contributing to the rate of evolution.

For Hardy-Weinberg Equilibrium to work for a population it must satisfy these conditions:
1) Large Population Size 2) No Migration 3) No Net Mutations 4) Random Mating 5) No Selection Although phenotypic evolution may seem to be accompanied by a change of habitat, the genetic variations are caused by changes to the DNA of the organisms and not directly to their physicality. The genetic information that is altered during evolution, an organism's DNA and RNA, is changed and carried on by transcription, translation, and replication. Mutations can occur during each of these steps that could affect an organism's fitness. Homologous structures show relations between non-extinct and extinct species. Phylogenetic trees and Cladograms can be used to diagram the gain or removal of a characteristic due to evolution. The closer that two species are to each other on these diagrams shows a closer relationship between the species than those that are shown farther apart. All
contemporary organisms
share the same basic units
of genetic coding,
DNA and/or RNA. Prezygotic Reproductive Barriers:
1) Habitat Isolation 2) Temporal Isolation
3) Behavioral Isolation 4) Mechanical
Isolation 5) Gametic Isolation Postzygotic Reproductive Barriers:
1) Reduced Hybrid Fertility 2) Reduced Hybrid Viability 3) Hybrid Breakdown To help put a timeline on the history of evolution, scientists use rock and fossil dating techniques as well as carbon dating. Doing so helps track the flow of genetic information and similarities between different species that could prove to be of relation with a common ancestor. Evidence that evolution is ongoing:
1) Chemical Resistance- bacteria become immune to our antibiotics and we have to create new ones.
2) Emergent Diseases- where'd those pathogens come from? they evolved!
3) Observed directional phenotypic changes in a population
4) A eukaryotic example that describes evolution of a structure or process Primitive Earth provided inorganic precursors from which organic molecules could have been synthesized due to the presence of available free energy and the absence of a significant quantity of oxygen.
Chemical Experiments have shown that it is possible to form complex organic molecules from inorganic molecules in the absence of life. The evolution of common structures shows that metabolic pathways are conserved across all currently recognized domains. Structural and functional evidence supports the relatedness of these domains. As a result of the relation between domains, all species are proven to have been affected by evolution. Genetic variation and mutation play roles in natural selection. A diverse gene pool is important for the survival of a species in a changing environment; competition for resources results in differential survival. An adaptation is a genetic variation that is favored by selection and is manifested as a trait that provides an advantage to an organism in a certain environment.
Adaption is linked to natural selection and genetic drift. Genetic drift is a nonselective process that greatly affects smaller populations. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar, a phosphate, and a nitrogen base. Nucleic acids, particularly DNA and RNA, have very complex properties such as their specific coding and the process they complete to become fully-functional DNA or RNA. The sugar and phosphate backbone need to fit perfectly. Nucleic acids also differ based on what function they are meant to perform and the function of the cell they are in.

When the order of these nucleic acids are not what they were intended to be, this is an example of a mutation. This can also occur if the sugars are not appropriately matched along the double helix.

Nucleic acids have ends, defined by the 3' and 5' carbons in the sugars of the nucleotide, that determines the direction in which complementary nucleotides are added during DNA synthesis, it also determines the direction of transcription. Nucleic acids are formed in such a specific way that only DNA can produce DNA. Through the process of transcription and DNA replication, with the assistance of many enzymes, new DNA is created starting from the 5' end toward the 3'.

Genetic diversity allows individuals in a population to respond differently to the same changes in environmental conditions.

With so many base pair and gene combinations occurring which creates genetic and biological diversity. When biological systems interact, these genes mix and become more diverse. This is what causes people to have different reactions to the same or similar environmental factors. If the genes prove useful that gene will most likely help the host survive and hopefully live to find a mate and be passed along to the future generations. A heterozygote may be more advantageous genotype than a homozygote under particular conditions, since with two different alleles, the organism has two forms of proteins that may provide functional resilience in response to environmental stresses. In some cases, having a recessive allele for a specific gene could help in protection or being unaffected by an environmental stress. This shoes that the interactions between biological systems cause different reactions formed from different genetic coding or DNA. These complex systems of nucleic acids and proteins folding accumulate to form enzymes. They help break down, speed up, and facilitate many cellular reactions throughout the body which thus connects the body. Allelic variation within a population can be modeled by the Hardy-Weinberg equation.
This equation helps explain how allele and genotypic frequencies in a population remain constant-that is, they are in equilibrium- from generation to generation unless specific disturbing influences are introduced through an equation. Proteins have an amino end and a carboxyl end, and consist on a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the carboxyl and amino groups of adjacent monomers.
Amino acids are connected to each other with these kinds of bonds and are folded to form more complex biological systems. In proteins, the specific order of amino acids in a polypeptide interacts with the environment to determine the overall shape of the protein, which also involves secondary, tertiary, and quaternary structure, and thus its function. The R group of an amino acid can be categorized by chemical properties and the interactions of these R groups determine structure and function of that region of the protein. DNA codes for specific amino acids and the order for each kind of protein that it forms Depending on environmental factors that other biological systems indirectly cause, it can cause the amino acids that are formed from the genetic code, DNA, to fold in specific patterns depending on its function. Ribosomes are small, universal structures comprised of two interactive parts: ribosomal RNA and protein. In a sequential manner, these cellular components interact to become the site of protein synthesis where the translation of genetic instructions yields different polypeptides. Ribosomes are what creates proteins from RNA. These ribosomes helps form proteins that make a biological more complex and its interactions with other systems cause the need for those proteins to survive and reproduce. Many copies of alleles or genes (gene duplication) may be the genesis of new phenotypes. When genes are replicated over and over, occasionally mutations or crossing over will occur and cause a change in the phenotype which creates the biodiversity and stems from a genetic code, DNA, within the biological system and how it interacts with other biological systems. Gene duplication creates a situation in which one copy of the gene maintains its original function while the duplicate may have evolved new functions. The genetic code for cells copies itself to grow and thus evolve. When a cell is singular it has a basic function, but as the cell density increases, each cell becomes more specialized and changes to help some of the biological system become increasingly more complex. For an enzyme-meditated reaction to occur, the substrate must be complementary to the surface properties of the active site. The shape of enzymes, active sites, and interaction with specific molecules are essential for the basic processes of the enzyme. NOW LET'S DOMINATE THE FINAL CELEBRATION!!!
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